[Pw_forum] Graphene Nanoribbon (Negative phonon frequencies and structure relaxation)

Ari P Seitsonen Ari.P.Seitsonen at iki.fi
Sat Jan 3 15:12:03 CET 2015


Dear Prabhakar,

   Ehmm, I might be wrong, but isn't this a zig-zag ribbon that your input 
produces (vertical lines for unit cell; the vertical-to-horisontal ratio 
not correct)::

    |
    | |
    C C C C C C C    <-- edge
     c c c c c c c
... c c c c c c c ...
    C C C C C C C    <-- edge
    | |

   The arm-chair would be

      |   |
      |CC |CC  CC      <-- edge
... cc  cc  cc  cc ...
      |CC |CC  CC      <-- edge
      |

   Then two issues: The zig-zag ribbon is spin-polarised 
(anti-ferromagnetic, the opposite edges with opposite spins) and now that 
I start to remember it, it might be that indeed this ribbon turns into two 
linear chains (five+ years since those calculations by Tobias...); please 
try with a wider one (or indeed the arm-chair ribbon).

     Greetings,

        apsi

PS Please remember to attach your affiliation to your mails

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
   Ari Paavo Seitsonen / Ari.P.Seitsonen at iki.fi / http://www.iki.fi/~apsi/
   Ecole Normale Supérieure (ENS), Département de Chimie, Paris
   Mobile (F) : +33 789 37 24 25    (CH) : +41 79 71 90 935


On Fri, 2 Jan 2015, Prabhakar Marepalli wrote:

> Dear Dr. Seitsonen,
> 
> Thanks for checking my script. You are right that the structure I posted runs in x-direction, but the problems I mentioned are exactly the same for this script too (I used y-notation as it is
> easier to draw and explain the unitcell that way). Also, thanks for pointing about the unitcell plane distance in z-direction. I've done the following changes:
> 
> 1) I've increased the lattice constant in z-direction to a very large value of 10 Angstroms, but it didn't change my answers by a lot.
> 
> 2) My structure is periodic in all directions, but I've picked the lattice vectors in y,z directions to be very long that the structure essentially acts like a 1D.
> 
> 3) I've added the 'ecutrho' parameter and picked a value of ecutrho=12*ecutwfc. This hasn't changed my answers either.
> 
> For relaxing, I've made the following changes to my original script:
> 
> &control
>    calculation='relax'
> 
> &ions
>    ion_dynamics='bfgs'
> 
> &cell
>    cell_dynamics='bfgs'
>    press_conv_thr=0.4,
>    cell_factor=3.0
> 
> The above relaxation almost changed my nanoribbon lattice to a square lattice. Can you please suggest if I'm using any of those parameters incorrectly?
> 
> Thanks,
> Prabhakar Marepalli
> 
> 
> 
> On Fri, Jan 2, 2015 at 1:16 PM, Ari P Seitsonen <Ari.P.Seitsonen at iki.fi> wrote:
>
>       Dear Prabhakar,
>
>         Did you check your structure? To me it looks very weird in 'XCrysDen', the planes of the periodic GNR's along z direction only 2 Angstroms apart. And yes, you should relax the
>       structure before calculating phonons. And your system is periodic in all directions, and the GNR seems to run along x, not y like I understood from your description below. Please also
>       read the instructions about 'ecutrho' when using ultra-soft pseudo potentials or the PAW method.
>
>           Good Luck, :)
>
>              apsi
>
>       -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
>         Ari Paavo Seitsonen / Ari.P.Seitsonen at iki.fi / http://www.iki.fi/~apsi/
>         Ecole Normale Supérieure (ENS), Département de Chimie, Paris
>         Mobile (F) : +33 789 37 24 25    (CH) : +41 79 71 90 935
> 
>
>       On Fri, 2 Jan 2015, Prabhakar Marepalli wrote:
>
>             Hello everyone,
>
>             I'm trying to compute phonon dispersion properties of graphene nanoribbon
>             using Quantum Espresso. My unit cell is a simple armchair structure with 4
>             atoms per unit cell. It looks like below:
>
>                    0----0
>                   /       \
>                  0        0
>
>             The above structure is replicated in the y-direction (the periodic
>             direction) while the x-direction is confined. Using the above structure,
>             here is the outline of the problems I'm running into:
>
>             1) Negative phonon frequencies (not only at gamma point, but at all other
>             k-points)
>
>             2) I tried using 'asr' but that doesn't seem to fix the problem.
>
>             3) I understand that the problem might be due to instability of the
>             structure (I did notice that the forces on atoms in scf calculation is
>             non-zero , forces of the magnitude 0.2 to 0.4).
>
>             4) When I try to relax the structure using 'ion_dynamics', the forces did go
>             down but the structure is relaxed so much that it is no longer graphene
>             nanoribbon.
>
>             Can you please give me some pointers on how to approach this problem, i.e.
>             how do I get rid of negative frequencies while relaxing the structure that
>             constrains it to look like a nanoribbon ?
>
>             Thanks for your time!
>
>             Here are my input files:
>
>             pw.x (this doesn't include the ion_dynamics relaxation).
>
>              &control
>                 calculation='scf'
>                 restart_mode='from_scratch',
>                 tstress = .true.
>                 tprnfor = .true.
>                 prefix='gnr_arm',
>                 pseudo_dir = '/work/02420/pm24229/QE/QE/pseudo/',
>                 outdir = '/home1/02420/pm24229/tmp/',
>              /
>              &system
>                 ibrav=  0, nat=  4, ntyp= 1, nbnd= 20,
>                 ecutwfc =25.0, occupations='smearing', smearing='marzari-vanderbilt',
>                 degauss=0.02
>              /
>              &electrons
>                 diagonalization='cg'
>                 conv_thr =  1.0d-12
>                 mixing_beta = 0.7
>              /
>             ATOMIC_SPECIES
>              C  12.0107  C.pbe-rrkjus.UPF
>
>             CELL_PARAMETERS {angstrom}
>              2.5546 0.00000000 0.00000000
>              0.00000000 10.0 0.00000000
>              0.00000000 0.00000000 2.00000000
>
>             ATOMIC_POSITIONS {angstrom}
>              C 0.0  0.0  0.0
>              C 1.2773 0.7375 0.000
>              C 1.2773 2.2125 0.00
>              C 0.0  2.95 0.0
>
>             K_POINTS automatic
>             20 1 1 1 1 1
>
>             ph.x
>
>             phonons on kspace
>              &inputph
>               tr2_ph=1.0d-14,
>               prefix='gnr_arm',
>               ldisp=.true.,
>               nq1=20, nq2=1, nq3=1
>               amass(1)=12.0107,
>               outdir='/home1/02420/pm24229/tmp/',
>               fildyn='gnr_dyn',
>              /
>
>             Thanks,
>             Prabhakar Marepalli
> 
> 
> 
> 
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